“I thought Space command has already been confirmed to function that way? To push the slot limit past 12?”

Tentative plan but ships will also have additional restrictions since hauling 5 SSDs along with your main party wouldn't exactly be good for balance. Still needs work, so it's hard to say with certainty how that will look.

Yeah, too much to really speculate now. Space combat will have to be pretty complex in order to do things like NPC crews as mentioned. I would recommend just waiting until a discussion is started properly with planning from our end.

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"On two occasions I have been asked,—"Pray, Mr. Babbage, if you put into the machine wrong figures, will the right answers come out?" I am not able rightly to apprehend the kind of confusion of ideas that could provoke such a question."
- Charles Babbage

Yeah I wouldn't even count on there being a refund of skill points if Space Command doesn't do what you want. You might think it would function like Infantry Command, but judging by how SWC has gone in the past, space stuff could be completely wonked up in the future. Instead of an SSD being 12 slots like now, for all we know an SSD/Home One could become a 72 slot ship and you gain 12 per point in Space Command. It could be that weird.
Or the skill could completely disappear!
No one will know for probably a few years yet.